JAL-2656 JAL-3615 check response headers to test for gzipped url reply

[jalview.git] / src / jalview / io / FileParse.java

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 7117d0f..167314e 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -35,10 +35,12 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.io.StringReader;
+import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -56,6 +58,7 @@ public class FileParse
 
   public File inFile = null;
 
+
   /**
    * a viewport associated with the current file operation. May be null. May
    * move to different object.
@@ -186,7 +189,7 @@ public class FileParse
       {
         try
         {
-          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataIn = getGzipReader(new FileInputStream(fileStr));
           dataName = fileStr;
           return error;
         } catch (Exception x)
@@ -204,7 +207,16 @@ public class FileParse
     return error;
   }
 
-  private BufferedReader tryAsGzipSource(InputStream inputStream)
+  /**
+   * Returns a {@code BufferedReader} which wraps the input stream with a
+   * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
+   * occurs or the compression method used is unsupported.
+   * 
+   * @param inputStream
+   * @return
+   * @throws Exception
+   */
+  private BufferedReader getGzipReader(InputStream inputStream)
           throws Exception
   {
     BufferedReader inData = new BufferedReader(
@@ -215,44 +227,58 @@ public class FileParse
     return inData;
   }
 
-  private boolean checkURLSource(String fileStr)
+  /**
+   * Tries to read from the given URL. If successful, saves a reader to the
+   * response in field {@code dataIn}, otherwise (on exception, or HTTP response
+   * status not 200), throws an exception.
+   * <p>
+   * If the response status includes
+   * 
+   * <pre>
+   * Content-Type : application/x-gzip
+   * </pre>
+   * 
+   * then tries to read as gzipped content.
+   * 
+   * @param urlStr
+   * @throws IOException
+   * @throws MalformedURLException
+   */
+  private void checkURLSource(String urlStr)
           throws IOException, MalformedURLException
   {
     errormessage = "URL NOT FOUND";
-    URL url = new URL(fileStr);
-    //
-    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
-    // Kenny Sabir
+    URL url = new URL(urlStr);
+    HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+    int rc = conn.getResponseCode();
+    if (rc != HttpURLConnection.HTTP_OK)
+    {
+      throw new IOException(
+              "Response status from " + urlStr + " was " + rc);
+    }
+    String encoding = conn.getContentEncoding();
+    String contentType = conn.getContentType();
+    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+            || "gzip".equals(encoding);
     Exception e = null;
-    if (fileStr.toLowerCase().endsWith(".gz"))
+    InputStream inputStream = conn.getInputStream();
+    if (isgzipped)
     {
       try
       {
-        InputStream inputStream = url.openStream();
-        dataIn = tryAsGzipSource(inputStream);
-        dataName = fileStr;
-        return false;
-      } catch (Exception ex)
-      {
-        e = ex;
-      }
-    }
-
-    try
-    {
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    } catch (IOException q)
-    {
-      if (e != null)
+        dataIn = getGzipReader(inputStream);
+        dataName = urlStr;
+      } catch (Exception e1)
       {
         throw new IOException(MessageManager
                 .getString("exception.failed_to_resolve_gzip_stream"), e);
       }
-      throw q;
+      return;
     }
-    // record URL as name of datasource.
-    dataName = fileStr;
-    return false;
+
+    dataIn = new BufferedReader(new InputStreamReader(inputStream));
+    dataName = urlStr;
+    return;
   }
 
   /**